Criteria Specification Registry

Criteria Specification (CSpec) Registry is intended to provide access to the Criteria Specifications used and applied by ClinGen Variant Curation Expert Panels and biocurators in the classification of variants.

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Criteria Specification

ClinGen PTEN Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for PTEN Version 1.0.0

Description : This version specified for the following genes: PTEN

Version : 1.0.0

PDF

PTEN VCEP

Released

8/17/2018

19:01:11

Rules for PTEN

Gene: PTEN (HGNC:9588) HGNC Name: phosphatase and tensin homolog Transcripts:

Criteria & Strength Specifications
PVS1 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Null variant (nonsense, frameshift, canonical +/−1 or 2 splice sites, initiation codon, single or multi-exon deletion) in a gene where loss of function (LOF) is a known mechanism of disease. Caveats: • Beware of genes where LOF is not a known disease mechanism (e.g. GFAP, MYH7). • Use caution interpreting LOF variants at the extreme 3’ end of a gene. • Use caution with splice variants that are predicted to lead to exon skipping but leave the remainder of the protein intact. • Use caution in the presence of multiple transcripts. Stand Alone Very Strong Null variant (nonsense, frameshift, canonical ±1 or 2 splice sites, initiation codon, single or multi-exon deletion) predicted to result in nonsense-mediated decay or causing truncation/frameshift at or 5’ to c.1121 (NM_000314.6). Modification Type: Disease-specific Strong Moderate Supporting Instructions: PTEN EP Specification: Follow SVI guidance, using PTEN-specific information. Per the PVS1 workflow guidance provided in Tayoun et al. 2018 (PMID 30192042), the following will apply: Nonsense, frameshift variants: PVS1 applies to variants predicted to result in nonsense-mediated decay (NMD); the predicted NMD cutoff for PTEN occurs at c.1121 (p.D375). For nonsense or frameshift variants at the 3’ end of the gene NOT predicted to result in nonsense-mediated decay, PVS1 may still be applied if the protein is disrupted at or 5’ to c.1121 (NM_000314.6). Please see supplementary information in manuscript for evidence supporting this cutoff. PVS1_Moderate applies to variants resulting in protein truncation 3’ of this cutoff. Splicing variants (+/- 1,2 intronic positions): Only apply to the variants resulting NMD (please refer to decision tree) OR entire exon deletion: Exons 1,2,4,5,6 OR 7 deletions OR multi-exon deletion: PVS1 (Resulting frameshift) Exons 3,8 OR 9 deletions: PVS1_Strong (in-frame but truncated/altered region is critical to protein function). Deletion (Single/multi exon to full gene): Please refer to decision tree. Duplication: Please refer to decision tree. Initiation codon: PVS1 applies to initiation codon variants. PTEN EP Commentary: No known alternative start codon in other transcripts. There are sufficient patients’ data from literature and labs support the pathogenicity of initiation codon variants. Not Applicable Comments: PTEN EP Specification: For nonsense or frameshift variants at the 3’ end of the gene NOT predicted to result in nonsense-mediated decay, PVS1 may still be applied if the protein is disrupted at or 5’ to c.1121 (NM_000314.6). Please see supplementary information in manuscript for evidence supporting this cutoff.
PS1 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Same amino acid change as a previously established pathogenic variant regardless of nucleotide change. Example: Val->Leu caused by either G>C or G>T in the same codon. Caveat: Beware of changes that impact splicing rather than at the amino acid/protein level. Stand Alone Very Strong Strong Same amino acid change as a previously established pathogenic variant regardless of nucleotide change OR different variant at same nucleotide position as a pathogenic splicing variant, where in silico models predict impact equal to or greater than the known pathogenic variant. Modification Type: Disease-specific Moderate Supporting Instructions: PTEN EP Specification: PS1 will be applied as described and expanded to include a different nucleotide substitution for an intronic splice site variant if the predicted impact is equal to or greater than the known pathogenic variant per in silico splicing tools. Caution should be used when applying this criteria to exonic variants causing aberrant splicing. Not Applicable Comments: PTEN EP Specification: PS1 will be applied as described and expanded to include a different nucleotide substitution for an intronic splice site variant if the predicted impact is equal to or greater than the known pathogenic variant per in silico splicing tools. Caution should be used when applying this criteria to exonic variants causing aberrant splicing.
PS2 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary De novo (both maternity and paternity confirmed) in a patient with the disease and no family history. Note: Confirmation of paternity only is insufficient. Egg donation, surrogate motherhood, errors in embryo transfer, etc. can contribute to non-maternity. Stand Alone Very Strong Two proven OR four assumed OR one proven + two assumed de novo observations in a patient with the disease and no family history. Modification Type: Strength Strong De novo (both maternity and paternity confirmed) observation in a patient with the disease and no family history. Modification Type: None Moderate Supporting Instructions: PS2_Very Strong: Two or more occurrences of PS2 OR two or more occurrences of PM6 AND one occurrence of PS2. Not Applicable
PS3 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product. Note: Functional studies that have been validated and shown to be reproducible and robust in a clinical diagnostic laboratory setting are considered the most well-established. Stand Alone Very Strong Strong Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product. Phosphatase activity <50% of wild-type RNA, mini-gene, or other assay shows impact on splicing Modification Type: Disease-specific Moderate Supporting Abnormal in vitro cellular assay or transgenic model with phenotype different from wild type that does not meet PS3. Modification Type: Disease-specific,Strength Instructions: PTEN EP Specification: PS3 may be applied to the following assays: In vitro or in vivo assay demonstrating ≥50% reduction in phosphatase activity compared to wild type control. Phosphatase assays for which criteria may be applied must include a catalytic dead control, such as p.C124S, as well as at least three biological replicates (Myers 1998, Stambolic 1998, Han 2000, Rodriguez-Escudero 2011, Costa 2015, Malek 2017). RNA, mini-gene, or other assay demonstrating an impact on splicing. PS3_Supporting: Abnormal in vitro cellular assay or transgenic model with phenotype different from wild-type that does not meet PS3. Examples of in vitro cellular assays to be considered for PS3_supporting evidence may include: Decreased PTEN or increased pAKT expression (Tan 2011, Spinelli 2015). Disruption of protein cellular localization (Lobo 2009, He 2012, Gil 2015). Aberrant cellular phenotypes, including defective cell migration, proliferation, and invasion (Costa 2015, Malek 2017). Not Applicable Comments: PTEN EP Specification: PS3 may be applied to the following assays: * In vitro or in vivo assay demonstrating >50% reduction in phosphatase activity compared to wild type control. Phosphatase assays for which criteria may be applied must include a catalytic dead control, such as p.C124S, as well as at least three biological replicates (Myers 1998, Stambolic 1998, Han 2000, Rodriguez-Escudero 2011, Costa 2015, Malek 2017). * RNA, mini-gene, or other assay demonstrating an impact on splicing. PS3_Supporting: Abnormal in vitro cellular assay or transgenic model with phenotype different from wild-type that does not meet PS3. Examples of in vitro cellular assays to be considered for PS3_supporting evidence may include: * Decreased PTEN or increased pAKT expression (Tan 2011, Spinelli 2015). * Disruption of protein cellular localization (Lobo 2009, He 2012, Gil 2015). * Aberrant cellular phenotypes, including defective cell migration, proliferation, and invasion (Costa 2015, Malek 2017)
PS4 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary The prevalence of the variant in affected individuals is significantly increased compared to the prevalence in controls. Note 1: Relative risk (RR) or odds ratio (OR), as obtained from case-control studies, is >5.0 and the confidence interval around the estimate of RR or OR does not include 1.0. See manuscript for detailed guidance. Note 2: In instances of very rare variants where case-control studies may not reach statistical significance, the prior observation of the variant in multiple unrelated patients with the same phenotype, and its absence in controls, may be used as moderate level of evidence. Stand Alone Very Strong Probands with specificity score ≥16 (see text). Modification Type: Strength Strong Probands with specificity score 4-15.5 (see text) OR The prevalence of the variant in affected individuals is significantly increased compared with the prevalence in controls. Modification Type: Strength Moderate Probands with specificity score of 2-3.5 (see text). Modification Type: Strength Supporting Phenotype specific for disease with single genetic etiology. Proband(s) with specificity score of 1-1.5 (see text). Modification Type: Disease-specific Instructions: PTEN EP Commentary: This criterion is unlikely to be used in this manner for a condition as rare as PHTS. However, if sufficiently powered, a case-control study finding an odds ratio ≥2 for a PHTS component phenotype with p<0.05 and 95% confidence interval with lower limit ≥1.5, this criteria may be applied. However, this criterion may not be applied in combination with PP4. Use 2: Patient’s phenotype or family history is highly specific for a disease with a single genetic etiology. PTEN EP Specifications: This criterion may not be applied if BS1 applies. Phenotype specificity scores are added across independent probands and calculated as follows: Adults: 1 point per proband with Cleveland Clinic (CC) score ≥30 (Tan 2011) 0.5 points per proband with CC score of 25-29. Children: 1 point per proband with pediatric phenotype score ≥5 (please see supplementary information in manuscript for scoring rubric). 0.5 points per proband with pediatric phenotype score of 4, but autism/developmental delay/intellectual disability may not contribute to the score. PS4_Very Strong: Probands with specificity score ≥16. PS4: Probands with specificity score of 4-15.5. PS4_Moderate: Probands with specificity score of 2-3.5. PS4_Supporting: Proband(s) with specificity score of 1-1.5. Not Applicable Comments: Use 1: The prevalence of the variant in affected individuals is significantly increased compared with the prevalence in controls. PTEN EP Commentary: This criterion is unlikely to be used in this manner for a condition as rare as PHTS. However, if sufficiently powered, a case-control study finding an odds ratio >2 for a PHTS component phenotype with p<0.05 and 95% confidence interval with lower limit >1.5, this criteria may be applied. However, this criterion may not be applied in combination with PP4. Use 2: Patient’s phenotype or family history is highly specific for a disease with a single genetic etiology. PTEN EP Specifications: This criterion may not be applied if BS1 applies. Phenotype specificity scores are added across independent probands and calculated as follows: * Adults: * 1 point per proband with Cleveland Clinic (CC) score >30 (Tan 2011) * 0.5 points per proband with CC score of 25-29. * Children: 1 point per proband with pediatric phenotype score >5 (please see supplementary information in manuscript for scoring rubric). * 0.5 points per proband with pediatric phenotype score of 4, but autism/developmental delay/intellectual disability may not contribute to the score. PS4_Very Strong: Probands with specificity score >16. PS4: Probands with specificity score of 4-15.5. PS4_Moderate: Probands with specificity score of 2-3.5. PS4_Supporting: Proband(s) with specificity score of 1-1.5.
PM1 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Located in a mutational hot spot and/or critical and well-established functional domain (e.g. active site of an enzyme) without benign variation. Stand Alone Very Strong Strong Moderate Located in a mutational hot spot and/or critical and well-established functional domain. Defined to include residues in catalytic motifs: 90-94, 123-130, 166-168 (NP_ 000305.3) Modification Type: Disease-specific Supporting Instructions: PTEN EP Specification: Defined to include residues in one of PTEN’s catalytic motifs, which include the WPD loop (residues 90-94), P-loop (also described as phosphatase core, residues 123-130), and the TI-loop (residues 166-168) (NP_ 000305.3) (Lee 1999). Not Applicable Comments: PTEN EP Specification: Defined to include residues in one of PTEN’s catalytic motifs, which include the WPD loop (residues 90-94), P-loop (also described as phosphatase core, residues 123-130), and the TI-loop (residues 166-168) (NP_ 000305.3) (Lee 1999).
PM2 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium. Caveat: Population data for indels may be poorly called by next generation sequencing. Stand Alone Very Strong Strong Moderate Present at <0.00001 (0.001%) allele frequency in gnomAD or another large sequenced population. If multiple alleles are present within any subpopulation, allele frequency in that subpopulation must be <0.00002 (0.002%). Modification Type: Disease-specific Supporting Instructions: PTEN EP Specification: Criteria may be applied if a variant is present at <0.00001 (0.001%) allele frequency in gnomAD or another large sequenced population. If multiple alleles are present within a subpopulation, allele frequency in that subpopulation must be <0.00002 (0.002%). Please see supplementary information in manuscript supporting application of PM2 for ultra-rare alleles. Not Applicable Comments: PTEN EP Specification: Criteria may be applied if a variant is present at <0.00001 (0.001%) allele frequency in gnomAD or another large sequenced population. If multiple alleles are present within a subpopulation, allele frequency in that subpopulation must be <0.00002 (0.002%). Please see supplementary information in manuscript supporting application of PM2 for ultra-rare alleles.
PM3 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary For recessive disorders, detected in trans with a pathogenic variant Note: This requires testing of parents (or offspring) to determine phase. Stand Alone Very Strong Strong Moderate Supporting Not Applicable Comments: For recessive disorders, detected in trans with a pathogenic variant.
PM4 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Protein length changes due to in-frame deletions/insertions in a non-repeat region or stop-loss variants. Stand Alone Very Strong Strong Moderate Protein length changes due to in-frame deletions/insertions in a non-repeat region or stop-loss variants. Applies to in-frame insertions or deletions impacting at least one residue in a catalytic motif (see PM1), protein truncation with disruption starting 3’ of c.1121 (NM_000314.6), and variants causing protein extension. Modification Type: Disease-specific Supporting Instructions: PTEN EP Specification: For in-frame insertions or deletions, criteria may apply only if the variant impacts at least one residue in one of the catalytic motifs specified in the PM1 criteria. Criteria will also apply for variants resulting in truncation 3’ to c.1121 (NM_000314.6) or variants resulting in protein extension, Not Applicable Comments: PTEN EP Specification: For in-frame insertions or deletions, criteria may apply only if the variant impacts at least one residue in one of the catalytic motifs specified in the PM1 criteria. Criteria will also apply for variants resulting in truncation 3’ to c.1121 (NM_000314.6) or variants resulting in protein extension.
PM5 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before. Example: Arg156His is pathogenic; now you observe Arg156Cys. Caveat: Beware of changes that impact splicing rather than at the amino acid/protein level. Stand Alone Very Strong Strong Moderate Missense change at an amino acid residue where a different missense change determined to be pathogenic or likely pathogenic has been seen before. In addition, variant being interrogated must have BLOSUM62 score equal to or less than the known variant. Modification Type: Disease-specific Supporting Instructions: PTEN EP Specifications: This rule may be applied when the known variant is likely pathogenic unless applying would lead to a higher (pathogenic) classification for the variant being assessed. The variant in question need not be novel but must have a BLOSUM62 (Henikoff 1992) score equal to or less than the known variant. Not Applicable Comments: PTEN EP Specifications: * This rule may be applied when the known variant is likely pathogenic unless applying would lead to a higher (pathogenic) classification for the variant being assessed. * The variant in question need not be novel but must have a BLOSUM62 (Henikoff 1992) score equal to or less than the known variant.
PM6 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Assumed de novo, but without confirmation of paternity and maternity. Stand Alone Very Strong Two proven OR four assumed OR one proven + two assumed de novo observations in a patient with the disease and no family history. Modification Type: Strength Strong Two probands with presumed de novo occurrence (maternity/ paternity not confirmed) with the disease and no family history. Modification Type: Strength Moderate Assumed de novo, but without confirmation of paternity and maternity, in proband with the disease and no family history. Modification Type: None Supporting Instructions: Assumed de novo, but without confirmation of paternity and maternity in a patient with the disease and no family history. PM6_Very Strong: Four or more occurrences of PM6 OR two occurrences of PM6 AND one occurrence of PS2. PM6_Strong: Two occurrences of PM6. Not Applicable Comments: PM6_Very Strong: Four or more occurrences of PM6 OR two occurrences of PM6 AND one occurrence of PS2. PM6_Strong: Two occurrences of PM6.
PP1 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease. Note: May be used as stronger evidence with increasing segregation data. Stand Alone Very Strong Strong Co-segregation with disease in multiple affected family members, with ≥7 meioses observed across at least two families. Modification Type: Strength Moderate Co-segregation with disease in multiple affected family members, with 5 or 6 meioses observed. Modification Type: Strength Supporting Co-segregation with disease in multiple affected family members, with 3 or 4 meioses observed. Modification Type: Disease-specific Instructions: PTEN EP Specification: Requires 3 or 4 meioses in order to apply. PP1_Strong: At least 7 meioses required across at least two families. PP1_Moderate: Requires 5 or 6 meioses in order to apply. Not Applicable Comments: PTEN EP Specification: Requires 3 or 4 meioses in order to apply. PP1_Strong: At least 7 meioses required across at least two families. PP1_Moderate: Requires 5 or 6 meioses in order to apply.
PP2 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Missense variant in a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease. Stand Alone Very Strong Strong Moderate Supporting Missense variant in a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease. Modification Type: None Not Applicable
PP3 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.). Caveat: As many in silico algorithms use the same or very similar input for their predictions, each algorithm should not be counted as an independent criterion. PP3 can be used only once in any evaluation of a variant. Stand Alone Very Strong Strong Moderate Supporting Multiple lines of computational evidence support a deleterious effect on the gene or gene product. To be applied only to synonymous or intronic variants where at least 2 out of 3 in silico models predict a splicing impact. Modification Type: Disease-specific Instructions: PTEN EP Specification: To be applied only to synonymous or intronic variants where at least 2 out of 3 in silico models predict a splicing impact. Not to be applied for variants which may impact the intron 1 splice donor or acceptor sites, and to be used cautiously for variants which may impact the intron 6 splice acceptor. PTEN EP Commentary: Given the lack of known benign or likely benign PTEN missense variants, the Expert Panel was unable to test the accuracy of in silico predictors to be used as evidence to apply BP4 or PP3 for PTEN missense variants. While investigating potential in silico tools, the Expert Panel also came to find that some algorithm predictions were highly sensitive to sequence alignment, further limiting confidence in these tools. Should the Expert Panel classify several missense variants as benign or likely benign, another attempt will be made to validate in silico tools to apply PP3/BP4 for missense variants. Please see supplementary information in manuscript detailing validation of splicing in silico tools and challenges presented by the specified donor/acceptor sites. Not Applicable Comments: PTEN EP Specification: To be applied only to synonymous or intronic variants where at least 2 out of 3 in silico models predict a splicing impact. Not to be applied for variants which may impact the intron 1 splice donor or acceptor sites, and to be used cautiously for variants which may impact the intron 6 splice acceptor. PTEN EP Commentary: Given the lack of known benign or likely benign PTEN missense variants, the Expert Panel was unable to test the accuracy of in silico predictors to be used as evidence to apply BP4 or PP3 for PTEN missense variants. While investigating potential in silico tools, the Expert Panel also came to find that some algorithm predictions were highly sensitive to sequence alignment, further limiting confidence in these tools. Should the Expert Panel classify several missense variants as benign or likely benign, another attempt will be made to validate in silico tools to apply PP3/BP4 for missense variants. Please see supplementary information in manuscript detailing validation of splicing in silico tools and challenges presented by the specified donor/acceptor sites.
PP4 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Patient’s phenotype or family history is highly specific for a disease with a single genetic etiology. Stand Alone Very Strong Strong Moderate Supporting Not Applicable Comments: PTEN EP Commentary: Phenotype specificity has been incorporated into the rule specifications for PS4 Use 2.
PP5
Original ACMG Summary Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory to perform an independent evaluation. Not Applicable This criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee. PubMed : 29543229
BA1 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Allele frequency is above 5% in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium. Stand Alone Allele frequency ≥0.01 (1%) in a studied population with ≥2,000 alleles tested and variant present in ≥5 alleles. Modification Type: Disease-specific Very Strong Strong Moderate Supporting Instructions: PTEN EP Specification: To be applied for variants with allele frequency ≥0.01 (≥1%) in a studied population with ≥2,000 alleles tested and variant present in ≥5 alleles. Please see supplementary information in manuscript for data supporting this lowered allele frequency threshold. Not Applicable
BS1 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Allele frequency is greater than expected for disorder. Stand Alone Very Strong Strong Allele frequency from 0.001 (0.1%) up to 0.01 (1%) in a studied population with ≥2,000 alleles tested and variant present in ≥5 alleles. Modification Type: Disease-specific Moderate Supporting Instructions: PTEN EP Specification: To be applied for variants with allele frequency of 0.001 up to 0.01 (0.1% up to 1%) in a studied population with ≥2,000 alleles tested and variant present in ≥5 alleles. Please see supplementary information in manuscript for data supporting this lowered allele frequency threshold. Not Applicable Comments: PTEN EP Specification: To be applied for variants with allele frequency of 0.001 up to 0.01 (0.1% up to 1%) in a studied population with >2,000 alleles tested and variant present in >5 alleles. Please see supplementary information in manuscript for data supporting this lowered allele frequency threshold. BS1_Supporting: To be applied for variants with allele frequency of 0.000043 up to 0.001 (0.0043% up to 0.1%) in a studied population with >2,000 alleles tested and variant present in >5 alleles. Threshold based on the approach published by Whiffin et al. (PMID 28518168) using the following values: * Prevalence: 1 in 9,000 (based on 15 disease-associated alleles present among the gnomAD population of ~135,000 individuals) * Allelic heterogeneity: 22/282 (based on prevalence of most common pathogenic PTEN variants, p.R130X and p.R335X, per Tan et al. PMID 21194675 and Bubien 2013 PMID 23335809) *Penetrance: 10% (overall cancer by age 40 for men with pathogenic germline PTEN variants is approximately 20% per Bubien 2013 PMID 23335809).
BS2 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age. Stand Alone Very Strong Strong Observed in the homozygous state in a healthy or PHTS-unaffected individual. One observation if homozygous status confirmed, two if not confirmed. To be applied at supporting evidence level if BS1 is also applied. Modification Type: Disease-specific Moderate Supporting Two homozygous observations with no clinical data provided, or meets criteria for BS2 but BS1 is also applied. Modification Type: Disease-specific,Strength Instructions: PTEN EP Specifications: Variant must be observed in the homozygous state in a healthy or PHTS-unaffected individual. Two independent observations are required if the homozygous status is not confirmed via parental testing. If BS1 is also applied, this criteria will be applied at the supporting evidence level to avoid a variant reaching benign status solely based on homozygous occurrences due to high population frequency (BS1+BS2). BS2_Supporting: Two homozygous observations with no clinical data provided, or meets criteria for BS2 but BS1 is also applied. Not Applicable Comments: PTEN EP Specifications: Variant must be observed in the homozygous state in a healthy or PHTS-unaffected individual. Two independent observations are required if the homozygous status is not confirmed via parental testing. If BS1 is also applied, this criteria will be applied at the supporting evidence level to avoid a variant reaching benign status solely based on homozygous occurrences due to high population frequency (BS1+BS2). BS2_Supporting: Two homozygous observations with no clinical data provided, or meets criteria for BS2 but BS1 is also applied.
BS3 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Well-established in vitro or in vivo functional studies show no damaging effect on protein function or splicing. Stand Alone Very Strong Strong Well-established in vitro or in vivo functional studies shows no damaging effect on protein function. To be applied for missense variants with both lipid phosphatase activity AND results from a second assay appropriate to the protein domain demonstrating no statistically significant difference from wild type. For intronic or synonymous variants, RNA, mini-gene or other splicing assay demonstrates no splicing impact. Modification Type: Disease-specific Moderate Supporting In vitro or in vivo functional study or studies showing no damaging effect on protein function but BS3 not met. Modification Type: Disease-specific,Strength Instructions: PTEN EP Specifications: BS3 may be applied to the following assays: For missense variants: Lipid phosphatase activity comparable to wild type in addition to a second assay appropriate to the protein domain demonstrating no statistically significant difference from wild type. Phosphatase assays for which criteria may be applied must include a catalytic dead control, such as p.C124S (NP_ 000305.3), as well as at least three biological replicates (Myers 1998, Stambolic 1998, Han 2000, Rodriguez-Escudero 2011, Costa 2015, Malek 2017). Examples of second assays may include: Decreased PTEN or increased pAKT expression (Tan 2011, Spinelli 2015). Disruption of protein cellular localization (Lobo 2009, He 2012, Gil 2015). Aberrant cellular phenotypes, including defective cell migration, proliferation, and invasion (Costa 2015, Malek 2017). For intronic or synonymous variants: RNA, mini-gene, or other assay demonstrate no impact on splicing. Not Applicable Comments: PTEN EP Specifications: BS3 may be applied to the following assays: * For missense variants: Lipid phosphatase activity comparable to wild type in addition to a second assay appropriate to the protein domain demonstrating no statistically significant difference from wild type. Phosphatase assays for which criteria may be applied must include a catalytic dead control, such as p.C124S (NP_ 000305.3), as well as at least three biological replicates (Myers 1998, Stambolic 1998, Han 2000, Rodriguez-Escudero 2011, Costa 2015, Malek 2017). Examples of second assays may include: * Decreased PTEN or increased pAKT expression (Tan 2011, Spinelli 2015). * Disruption of protein cellular localization (Lobo 2009, He 2012, Gil 2015). * Aberrant cellular phenotypes, including defective cell migration, proliferation, and invasion (Costa 2015, Malek 2017). * For intronic or synonymous variants: RNA, mini-gene, or other assay demonstrate no impact on splicing. BS3_Supporting: In vitro or in vivo functional study or studies showing no damaging effect on protein function but BS3 not met.
BS4 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Lack of segregation in affected members of a family. Caveat: The presence of phenocopies for common phenotypes (i.e. cancer, epilepsy) can mimic lack of segregation among affected individuals. Also, families may have more than one pathogenic variant contributing to an autosomal dominant disorder, further confounding an apparent lack of segregation. Stand Alone Very Strong Strong Lack of segregation in affected members of two or more families. Modification Type: Disease-specific Moderate Supporting Lack of segregation in affected members of one family. Modification Type: Disease-specific,Strength Instructions: PTEN EP Specification: BS4: Two or more families are require for strong evidence level. BS4_Supporting: Lack of segregation in one family. Not Applicable Comments: PTEN EP Specification: Two or more families are require for strong evidence level.
BP1 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Missense variant in a gene for which primarily truncating variants are known to cause disease. Stand Alone Very Strong Strong Moderate Supporting Not Applicable Comments: This rule is not applicable to PTEN.
BP2 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Observed in trans with a pathogenic variant for a fully penetrant dominant gene/disorder or observed in cis with a pathogenic variant in any inheritance pattern. Stand Alone Very Strong Strong Moderate Supporting Observed in trans with a pathogenic or likely pathogenic PTEN variant OR at least three observations in cis and/or phase unknown with different pathogenic/likely pathogenic PTEN variants. Modification Type: Disease-specific Instructions: PTEN EP Specifications: The other variant may be either pathogenic or likely pathogenic. This rule may also be applied for at least three observations of the variant in cis or unknown phase with different pathogenic or likely pathogenic PTEN variants. Not Applicable Comments: PTEN EP Specifications: The other variant may be either pathogenic or likely pathogenic. This rule may also be applied for at least three observations of the variant in cis or unknown phase with different pathogenic or likely pathogenic PTEN variants.
BP3 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary In frame-deletions/insertions in a repetitive region without a known function. Stand Alone Very Strong Strong Moderate Supporting Not Applicable Comments: This rule is not applicable to PTEN.
BP4 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc) Caveat: As many in silico algorithms use the same or very similar input for their predictions, each algorithm cannot be counted as an independent criterion. BP4 can be used only once in any evaluation of a variant. Stand Alone Very Strong Strong Moderate Supporting Multiple lines of computational evidence suggest no impact on gene or gene product. To be applied only to synonymous or intronic variants where at least 2 out of 3 in silico models predict no splicing impact. Modification Type: Disease-specific Instructions: PTEN EP Specification: To be applied only to synonymous or intronic variants where at least 2 out of 3 in silico models predict no splicing impact. Not to be applied for variants which may impact the intron 1 splice donor or acceptor sites, and to be used cautiously for variants which may impact the intron 6 splice acceptor. PTEN EP Commentary: Please see PP3 commentary. Given the lack of known benign or likely benign PTEN missense variants, the Expert Panel was unable to test the accuracy of in silico predictors to be used as evidence to apply BP4 or PP3 for PTEN missense variants. While investigating potential in silico tools, the Expert Panel also came to find that some algorithm predictions were highly sensitive to sequence alignment, further limiting confidence in these tools. Should the Expert Panel classify several missense variants as benign or likely benign, another attempt will be made to validate in silico tools to apply PP3/BP4 for missense variants. Please see supplementary information in manuscript detailing validation of splicing in silico tools and challenges presented by the specified donor/acceptor sites. Not Applicable Comments: PTEN EP Specification: To be applied only to synonymous or intronic variants where at least 2 out of 3 in silico models predict no splicing impact. Not to be applied for variants which may impact the intron 1 splice donor or acceptor sites, and to be used cautiously for variants which may impact the intron 6 splice acceptor. PTEN EP Commentary: Please see PP3 commentary.
BP5 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary Variant found in a case with an alternate molecular basis for disease. Stand Alone Very Strong Strong Moderate Supporting Variant found in a case with an alternate molecular basis for disease. Other gene/disorder must be considered highly penetrant AND patient’s personal/family history must demonstrate no overlap between other gene and PTEN. Modification Type: Disease-specific Instructions: PTEN EP Specifications: At least two such cases are required for criteria to apply. In addition, the other gene/disorder must be considered highly penetrant AND the patient’s personal/family history must demonstrate no overlap between the other gene and PTEN. Not Applicable Comments: PTEN EP Specifications: At least two such cases are required for criteria to apply. In addition, the other gene/disorder must be considered highly penetrant AND the patient’s personal/family history must demonstrate no overlap between the other gene and PTEN.
BP6
Original ACMG Summary Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation. Not Applicable This criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee. PubMed : 29543229
BP7 PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Files References
Original ACMG Summary A synonymous variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved. Stand Alone Very Strong Strong Moderate Supporting A synonymous (silent) or intronic variant at or beyond +7/-21 for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved. Modification Type: Disease-specific Instructions: PTEN EP Specification: Intronic variants must be positioned at or beyond +7/-21. Nucleotide may be defined as “not conserved” with PhastCons score <1 and PhyloP score <0.1. Not Applicable Comments: PTEN EP Specification: Intronic variants must be positioned at or beyond +7/-21. Nucleotide may be defined as “not conserved” with PhastCons score <1 and PhyloP score <0.1.

Rules for Combining Criteria

Pathogenic

1 Very Strong (PVS1, PS2_Very Strong, PS4_Very Strong, PM6_Very Strong) AND ≥ 1 Strong (PS1, PS2, PS3, PS4, PM6_Strong, PP1_Strong)

1 Very Strong (PVS1, PS2_Very Strong, PS4_Very Strong, PM6_Very Strong) AND ≥ 2 Moderate (PS4_Moderate, PM1, PM2, PM4, PM5, PM6, PP1_Moderate)

1 Very Strong (PVS1, PS2_Very Strong, PS4_Very Strong, PM6_Very Strong) AND 1 Moderate (PS4_Moderate, PM1, PM2, PM4, PM5, PM6, PP1_Moderate) AND 1 Supporting (PS3_Supporting, PS4_Supporting, PP1, PP2, PP3)

1 Very Strong (PVS1, PS2_Very Strong, PS4_Very Strong, PM6_Very Strong) AND ≥ 2 Supporting (PS3_Supporting, PS4_Supporting, PP1, PP2, PP3)

≥ 2 Strong (PS1, PS2, PS3, PS4, PM6_Strong, PP1_Strong)

1 Strong (PS1, PS2, PS3, PS4, PM6_Strong, PP1_Strong) AND ≥ 3 Moderate (PS4_Moderate, PM1, PM2, PM4, PM5, PM6, PP1_Moderate)

1 Strong (PS1, PS2, PS3, PS4, PM6_Strong, PP1_Strong) AND 2 Moderate (PS4_Moderate, PM1, PM2, PM4, PM5, PM6, PP1_Moderate) AND ≥ 2 Supporting (PS3_Supporting, PS4_Supporting, PP1, PP2, PP3)

1 Strong (PS1, PS2, PS3, PS4, PM6_Strong, PP1_Strong) AND 1 Moderate (PS4_Moderate, PM1, PM2, PM4, PM5, PM6, PP1_Moderate) AND ≥ 4 Supporting (PS3_Supporting, PS4_Supporting, PP1, PP2, PP3)

Likely Pathogenic

1 Very Strong (PVS1, PS2_Very Strong, PS4_Very Strong, PM6_Very Strong) AND 1 Moderate (PS4_Moderate, PM1, PM2, PM4, PM5, PM6, PP1_Moderate)

1 Strong (PS1, PS2, PS3, PS4, PM6_Strong, PP1_Strong) AND 1 Moderate (PS4_Moderate, PM1, PM2, PM4, PM5, PM6, PP1_Moderate)

1 Strong (PS1, PS2, PS3, PS4, PM6_Strong, PP1_Strong) AND ≥ 2 Supporting (PS3_Supporting, PS4_Supporting, PP1, PP2, PP3)

≥ 3 Moderate (PS4_Moderate, PM1, PM2, PM4, PM5, PM6, PP1_Moderate)

2 Moderate (PS4_Moderate, PM1, PM2, PM4, PM5, PM6, PP1_Moderate) AND ≥ 2 Supporting (PS3_Supporting, PS4_Supporting, PP1, PP2, PP3)

1 Moderate (PS4_Moderate, PM1, PM2, PM4, PM5, PM6, PP1_Moderate) AND ≥ 4 Supporting (PS3_Supporting, PS4_Supporting, PP1, PP2, PP3)

1 Strong (PS1, PS2, PS3, PS4, PM6_Strong, PP1_Strong) AND 2 Moderate (PS4_Moderate, PM1, PM2, PM4, PM5, PM6, PP1_Moderate)

Benign

≥ 2 Strong (BS1, BS2, BS3, BS4)

1 Stand Alone (BA1)

Likely Benign

1 Strong (BS1, BS2, BS3, BS4) AND 1 Supporting (BS2_Supporting, BS3_Supporting, BS4_Supporting, BP2, BP4, BP5, BP7)

≥ 2 Supporting (BS2_Supporting, BS3_Supporting, BS4_Supporting, BP2, BP4, BP5, BP7)

References

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